AMICI v0.28.0

Breaking changes

• Changed the default steady-state method to integrationOnly (by @dweindl in #2574)

  The default mode for computing steady states and sensitivities at steady state was changed to integrationOnly (from previously integrateIfNewtonFails).

  This was done for a more robust default behavior. For example, the evaluation in https://doi.org/10.1371/journal.pone.0312148 shows that - at least for some models - Newton's method may easily lead to physically impossible solutions.

  To keep the previous behavior, use:

  amici_model.setSteadyStateComputationMode(amici.SteadyStateComputationMode.integrateIfNewtonFails)
  amici_model.setSteadyStateSensitivityMode(amici.SteadyStateSensitivityMode.integrateIfNewtonFails)

Fixes

• PEtab import: Fixed potentially incorrect sensitivities with observable/state-dependent sigmas.
  This was fixed for all cases amici can handle, others cases will now result in ValueErrors (#2563).

  by @dweindl in #2562

• Fixed potentially incorrect disabling of Newton's method

  by @dweindl in #2576

• Fixed ModelStateDerived copy ctor, where previously dangling pointers could lead to crashes in some situations

  by @dweindl in #2583

• Added missing simulation status codes

  by @dweindl in #2560

• Check for unsupported observable IDs in sigma expressions

  by @dweindl in #2563

Features

• Optional warning in fill_in_parameters

  by @dweindl in #2578

Full Changelog: v0.27.0...v0.28.0

AMICI v0.27.0

This release comes with an updated version of the SUNDIALS package (7.1.1) (#2513).
For C++ users of some of AMICI's internal RAII classes, this may include some breaking changes.
The Python API is not affected.

Note regarding editable installations (pip install -e ...): Due to the SUNDIALS update, it will be necessary to clean out some temporary build directories (at least ThirdParty/sundials/build/, python/sdist/build/) before rebuilding the package.

Fixes

• Fixed a bug that led to program termination if a root-after-reinitialization
  error (potentially also others) occurred at an output timepoint

  by @dweindl in #2555

• CMake: Fixes compilation errors for models named model

  by @dweindl in #2547

• Updated CMake export config, making it easier to use AMICI in CMake projects
  and fixing some potential issues with interferring packages

  by @dweindl in #2540

• CMake: Set policies for CMake 3.31

  by @dweindl in #2539

• Documentation fixes by @FFroehlich, @ChocolateCharlie, @dweindl

Full Changelog: v0.26.3...v0.27.0

AMICI v0.26.3

Fixes

• Skip building SuiteSparse shared libraries and build all subprojects together for slightly faster package installation

  by @dweindl in #2514 and #2519

• Got rid of petab DeprecationWarnings when using the amici_import_petab CLI

  by @dweindl in #2517

• Now also sundials and suitesparse are built in debug mode when installing with ENABLE_AMICI_DEBUGGING=TRUE

  by @dweindl in #2515

Full Changelog: v0.26.2...v0.26.3

AMICI v0.26.2

Fixes

• Fixed a sympy float comparison issue in spline code that would cause an AssertionError

  by @dweindl in #2499

• Fixed some warnings from recent CMake versions

  by @dweindl in #2492

• Fixed a potential issue when including AMICI in a CMake project

  by @dweindl in #2493

Full Changelog: v0.26.1...v0.26.2

AMICI v0.26.1

Fixes

• Fixed some C++ exception handling that previously could crash Python under certain conditions

  by @dweindl in #2484

• Disabled turning warnings into errors when building amici on GitHub Actions in downstream projects

  by @dweindl in #2481

• Fixed CMP0167 warning with CMake 3.30

  by @dweindl in #2480

AMICI v0.26.0

AMICI v0.26.0 requires sympy>=1.12.1 and petab>=0.4.0.

Policy changes

• Updated AMICI's versioning / deprecation policy

  We will start removing deprecated features that had a deprecation warning
  for longer than six months in the next minor release.

Deprecations

• Passing individual tables to amici_import_petab is now deprecated.
  Use a petab.Problem instance instead.

  by @dweindl in #2464

Fixes

• Fixed a bug where during installation of AMICI, an incorrect sundials CMake
  would be used resulting in installation errors.

  by @dweindl in #2468

Full Changelog: v0.25.2...v0.26.0

AMICI v0.25.2

Fixes

• Fixed a bug in PEtab import which led to incorrect gradients
  w.r.t. estimated initial values specified via the condition table
  BREAKING CHANGE:
  amici.petab.sbml_import.{import_model_sbml,import_model} no longer supports
  passing individual PEtab tables, but only the PEtab problem object.
  This functionality was deprecated since v0.12.0 (2022-08-26).
• Fixes for numpy 2.0 compatibility
  NOTE: As long as some amici dependencies don't support numpy 2.0 yet,
  you may need to pin numpy to <2.0 in your requirements
  (pip install amici "numpy<2.0").

Full Changelog: v0.25.1...v0.25.2

AMICI v0.25.1

Fixes

• Avoid clashes with sympy-entities in plot_expressions
  by @dweindl in #2440
• PEtab: fix KeyErrors for missing parameters in fill_in_parameters
  (default values are now used if only a subset of parameters is provided)
  by @dweindl in #2449
• CMake: Fix Intel MKL detection when not using environment modules
  by @dweindl in #2443
• CMake: Fix some issues with multi-config generators
  by @dweindl in #2445

Full Changelog: v0.25.0...v0.25.1

AMICI v0.25.0

This release requires Python >= 3.10.

Fixes

• Fixed a bug in event handling that could lead to incorrect simulation
  results for models with events that assign to compartments and have
  additional event assignments
  by @dweindl in #2428
• SBML import: handle useValuesFromTriggerTime attribute on events.
  This attribute was previously ignored. It is possible that now AMICI fails
  to import models that it previously imported successfully. For cases where
  useValuesFromTriggerTime=True made a difference, AMICI might have produced
  incorrect results before.
  by @dweindl in #2429
• Faster code generation for models with events if they don't have
  state-dependent triggers
  by @dweindl in #2417
• Most warnings now come with a more informative code location
  by @dweindl in #2421
• amici.ExpData was changed so that isinstance(edata, amici.ExpData) works
  by @dweindl in #2396

Features

• Event-assignments to compartments are now supported. Previously, this only
  worked for compartments that were rate rule targets.
  by @dweindl in #2425
• Releases are now deployed to Docker Hub
  by @dweindl in #2413

Full Changelog: v0.24.0...v0.25.0

AMICI v0.24.0

This will be the last release supporting Python 3.9.
Future releases will require Python 3.10.

Fixes

• Fix cmake error cannot create directory: /cmake/Amici
  during model import in cases where BLAS was not found via FindBLAS
  by @dweindl in #2389
• Added status code AMICI_CONSTR_FAIL
  by @dweindl in #2379
• Fixed certain initial state issues with PEtab
  by @dweindl in #2382
• Fixed Solver operator== and copyctor
  (constraints were not copied correctly)
  by @dweindl in #2388
• Avoid confusing warnings about non-finite timepoints
  by @dweindl in #2395
• Fixed incorrect exception types / messages for IDASolver
  by @dweindl in #2398
• cmake: set SUNDIALS path hint for python package to help CMake find
  the correct SUNDIALS installation
  by @dweindl in #2397

Features

• Optionally include measurements in plot_observable_trajectories
  by @dweindl in #2381
• Improved type annotations in swig-wrappers
  by @dweindl in #2401
• Additional attributes are accessible directly via ReturnDataView and
  ExpDataView, e.g. ReturnDataView.ny, ReturnDataView.nx
  by @dweindl in #2405
• Allow subselection of state variables for convergence check during
  steady-state simulations via Model.set_steadystate_mask([1, 0, ..., 1])
  (positive value: check; non-positive: don't check).
  by @dweindl in #2387

Full Changelog: v0.23.1...v0.24.0